Evaluation of the prognostic significances of γ-secretase genes in pancreatic cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30944650", "kind": "science-record", "revision": 7, "content_hash": "sha256:269cc6cd02caf39072188851a7c7c78a70c66185c5bbe135be1d0eb0cef2e2cb", "created_at": "2026-11-01T15:40:44Z", "updated_at": "2026-11-01T22:00:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Evaluation of the prognostic significances of γ-secretase genes in pancreatic cancer.", "doi": "10.3892/ol.2019.10113", "pmid": "30944650", "authors": ["Yun Ho Jeon", "Mihyang Ha", "Sung Won Kim", "Mun Ju Kim", "Chi-Seung Lee", "Chang-Kyu Oh", "Myoung-Eun Han", "Sae-Ock Oh", "Yun Hak Kim"], "journal": "Oncology letters", "year": 2019, "abstract": "With the growing requirement for novel prognostic biomarkers for pancreatic cancer, many studies have focused on clinical and/or genomic variables. Although many studies have been performed, carbohydrate antigen 19-9 is the only biomarker in clinical use. Therefore, the present study examined whether γ-secretase genes, including presenilin (PSEN), nicastrin (NCSTN), presenilin enhancer protein 2 (PSENEN), and anterior pharynx-defective 1 (APH1-), could serve as prognostic factors for pancreatic cancer. The cohorts selected included >100 pancreatic cancer patients. Patient data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GSE21501). The prognostic roles of the γ-secretase genes were analyzed by several survival analysis methods. Among the γ-secretase genes, the prognosis tended to be worse in the 2 cohorts with increasing expression of PSEN1, APH1A, and PSENEN, while the remaining genes were the opposite in the 2 cohorts. Notably, although the patient characteristics were quite different, APH1A was statistically significantly associated with prognosis in the 2 cohorts. The hazard ratio of APH1A for overall survival was 1.598 (TCGA) and 2.724 (GSE21501). These results contribute to the study of γ-secretase in pancreatic cancer. We believe that γ-secretase, particularly APH1A, will be a new prognostic biomarker for pancreatic cancer.", "claims": [{"id": "claim-method", "statement": "To identify the discriminatory power of γ-secretase genes as a categorical variable, we analyzed Kaplan-Meier curves with log-rank test for gene expression and survival.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30944650", "locator": "sections[9] \"Survival curve of γ-secretases\" paragraph 2", "quote": "To identify the discriminatory power of γ-secretase genes as a categorical variable, we analyzed Kaplan-Meier curves with log-rank test for gene expression and survival."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30944650", "locator": "sections[15] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:30944650"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE15471"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE15471"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30944650", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/ol.2019.10113", "sha256": 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pancreas, 2 cm < diameter ≤4 cm", "−", "16"], ["T3", "Confined to the pancreas, >4 cm in diameter", "−", "79"], ["T4", "Extends outside the pancreas and into nearby major blood vessels", "−", "1"], ["N0", "No spread to nearby lymph nodes", "−", "28"], ["N1", "Spreads to no more than 3 nearby lymph nodes", "−", "73"]], "row_count": 13, "column_count": 4, "numeric_cells": 17, "header_rows": 1, "locator": "section[8]/table-wrap[1]#tI-ol-0-0-10113"}}, {"id": "asset:table:pmid:30944650:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:acd87bf48caa67265b4a7e8acdab070f4f7e41c0766b13d81ca85d2af7162722", "bytes": 948, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#tII-ol-0-0-10113", "version": null, "note": "Number of patients (event) divided by each gene cutoff value.", "structure": {"pmcid": "PMC6444455", "section_index": 9, "section_title": "Survival curve of γ-secretases", "row_count": 14, "column_count": 4}, "table": {"label": "Table II.", "caption": "Number of patients (event) divided by each gene cutoff value.", "rows": [["Gene", "Group", "TCGA", "GSE21501"], ["Total values (n)", "All patients", "172", "102"], ["PSEN1", "High expression (event)", "107 (68)", "61 (42)"], ["", "Low expression (event)", "65 (24)", "41 (24)"], ["APH1A", "High expression (event)", "75 (49)", "68 (49)"], ["", "Low expression (event)", "97 (43)", "34 (17)"], ["PSENEN", "High expression (event)", "101 (57)", "56 (40)"], ["", "Low expression (event)", "71 (35)", "46 (26)"], ["NCSTN", "High expression (event)", "127 (74)", "57 (38)"], ["", "Low expression (event)", "45 (18)", "45 (28)"], ["PSEN2", "High expression (event)", "79 (39)", "86 (59)"], ["", "Low expression (event)", "93 (53)", "16 (7)"], ["APH1B", "High expression (event)", "37 (10)", "69 (47)"], ["", "Low expression (event)", "135 (82)", "33 (19)"]], "row_count": 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"0.00291b", "2.0355", "1.275", "3.25"], ["APH1A", "0.025a", "1.598", "1.061", "2.408"], ["PSENEN", "0.26", "1.275", "0.8353", "1.946"], ["NCSTN", "0.0469a", "1.7011", "1.007", "2.873"], ["PSEN2", "0.0782", "1.4574", "0.9583", "2.216"], ["APH1B", "<0.0001c", "3.2734", "1.691", "6.335"], [""], ["B, GSE21501"], [""], ["Genes", "P-value", "Hazard ratio", "95% confidence interval"], [""], ["PSEN1", "0.0835", "1.5772", "0.9414", "2.642"], ["APH1A", "<0.0001c", "2.724", "1.517", "4.892"], ["PSENEN", "0.0248a", "1.7894", "1.076", "2.975"], ["NCSTN", "0.371", "1.257", "0.7623", "2.071"], ["PSEN2", "0.195", "1.747", "0.7517", "4.06"], ["APH1B", "0.153", "1.4939", "0.861", "2.592"]], "row_count": 20, "column_count": 5, "numeric_cells": 51, "header_rows": 3, "locator": "section[9]/table-wrap[2]#tIII-ol-0-0-10113"}}, {"id": "asset:table:pmid:30944650:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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